chr17-19533822-G-T

Variant names:

• chr17-19533822-G-T
• rs72466470
• ENST00000571335.5:c.-311+251G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000571335.5(SLC47A1):​c.-311+251G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000784 in 1,148,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000021 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000060 (0 hom.)
• Consequence: SLC47A1 ENST00000571335.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 2 publications found

Genes affected

SLC47A1 (HGNC:25588): (solute carrier family 47 member 1) This gene is located within the Smith-Magenis syndrome region on chromosome 17. It encodes a protein of unknown function. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A1	NM_018242.3	c.-118G>T		upstream_gene_variant		ENST00000270570.8	NP_060712.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC47A1	ENST00000270570.8	c.-118G>T		upstream_gene_variant		1	NM_018242.3	ENSP00000270570.4

Frequencies

GnomAD3 genomes AF: 0.0000210 AC: 3 AN: 143106 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000253

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000704

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000158

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000597 AC: 6 AN: 1004940 Hom.: 0 Cov.: 17 AF XY: 0.00000841 AC XY: 4 AN XY: 475420

African (AFR) AF: 0.00 AC: 0 AN: 21082

American (AMR) AF: 0.000139 AC: 1 AN: 7182

Ashkenazi Jewish (ASJ) AF: 0.0000781 AC: 1 AN: 12800

East Asian (EAS) AF: 0.00 AC: 0 AN: 24532

South Asian (SAS) AF: 0.00 AC: 0 AN: 19568

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19508

Middle Eastern (MID) AF: 0.000373 AC: 1 AN: 2678

European-Non Finnish (NFE) AF: 0.00000350 AC: 3 AN: 857760

Other (OTH) AF: 0.00 AC: 0 AN: 39830

GnomAD4 genome AF: 0.0000210 AC: 3 AN: 143106 Hom.: 0 Cov.: 31 AF XY: 0.0000286 AC XY: 2 AN XY: 69986

African (AFR) AF: 0.0000253 AC: 1 AN: 39572

American (AMR) AF: 0.0000704 AC: 1 AN: 14212

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3320

East Asian (EAS) AF: 0.00 AC: 0 AN: 5022

South Asian (SAS) AF: 0.00 AC: 0 AN: 4720

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9988

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000158 AC: 1 AN: 63218

Other (OTH) AF: 0.00 AC: 0 AN: 1964

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	18
DANN	Benign	0.95
PhyloP100		1.5
PromoterAI		-0.51	Under-expression

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs72466470; hg19: chr17-19437135;